Abstract
Maturation of transfer RNA molecules often requires removal of intronic sequences by endonucleases that recognize diverse RNA secondary structures. Archaeal splicing endonucleases [versatile RNA-splicing endonucleases (VSENs)] exhibit remarkable substrate versatility, yet the structural basis for this broad specificity has remained unclear. Here, we report the 1.8-Å crystal structure of ARMAN-2, an ϵ2-type VSEN from Candidatus Micrarchaeum acidiphilum, in complex with a synthetic bulge-helix-bulge RNA. The structure reveals that a lineage-specific insertion, the ARMAN-specific loop (ASL), interacts with the bulged region of the RNA and helps to orient the scissile phosphate for catalysis via conserved tyrosine and lysine residues. Functional assays confirmed the essential role of the ASL in substrate binding and cleavage. Structural comparisons with (αβ)2-type Crenarchaeal VSENs, which contain a distinct Crenarchaea-specific loop (CSL), and with a eukaryotic equivalent, the TSEN complex, which harbors a previously uncharacterized eukaryotic-specific loop (ESL), uncovered mechanistic convergence across domains of life. We show that the ESL occupies a position analogous to the ASL and CSL, and likely supports bulge stabilization in long introns. These findings establish a mechanistic model for broad substrate recognition by VSENs and suggest that loop-mediated RNA positioning co-evolved with intron complexity in archaeal and eukaryotic lineages.